Lowest electronic states of the CP47 antenna protein complex of photosystem II: simulation of optical spectra and revised structural assignments

PigmentHunter: A point-and-click application for automated chlorophyll-protein simulations

Chlorophyll proteins (CPs) are the workhorses of biological photosynthesis, working together to absorb solar energy, transfer it to chemically active reaction centers, and control the charge-separation process that drives its storage as chemical energy. Yet predicting CP optical and electronic properties remains a serious challenge, driven by the computational difficulty of treating large, electronically coupled molecular pigments embedded in a dynamically structured protein environment. To address this challenge, we introduce here an analysis tool called PigmentHunter, which automates the process of preparing CP structures for molecular dynamics (MD), running short MD simulations on the nanoHUB.org science gateway, and then using electrostatic and steric analysis routines to predict optical absorption, fluorescence, and circular dichroism spectra within a Frenkel exciton model. Inter-pigment couplings are evaluated using point-dipole or transition-charge coupling models, while site energies can be estimated using both electrostatic and ring-deformation approaches. The package is built in a Jupyter Notebook environment, with a point-and-click interface that can be used either to manually prepare individual structures or to batch-process many structures at once. We illustrate PigmentHunter's capabilities with example simulations on spectral line shapes in the light harvesting 2 complex, site energies in the Fenna-Matthews-Olson protein, and ring deformation in photosystems I and II.

High-Resolution Frequency-Domain Spectroscopic and Modeling Studies of Photosystem I (PSI), PSI Mutants and PSI Supercomplexes

Photosystem I (PSI) is one of the two main pigment-protein complexes where the primary steps of oxygenic photosynthesis take place. This review describes low-temperature frequency-domain experiments (absorption, emission, circular dichroism, resonant and non-resonant hole-burned spectra) and modeling efforts reported for PSI in recent years. In particular, we focus on the spectral hole-burning studies, which are not as common in photosynthesis research as the time-domain spectroscopies. Experimental and modeling data obtained for trimeric cyanobacterial Photosystem I (PSI3), PSI3 mutants, and PSI3-IsiA18 supercomplexes are analyzed to provide a more comprehensive understanding of their excitonic structure and excitation energy transfer (EET) processes. Detailed information on the excitonic structure of photosynthetic complexes is essential to determine the structure-function relationship. We will focus on the so-called "red antenna states" of cyanobacterial PSI, as these states play an important role in photochemical processes and EET pathways. The high-resolution data and modeling studies presented here provide additional information on the energetics of the lowest energy states and their chlorophyll (Chl) compositions, as well as the EET pathways and how they are altered by mutations. We present evidence that the low-energy traps observed in PSI are excitonically coupled states with significant charge-transfer (CT) character. The analysis presented for various optical spectra of PSI3 and PSI3-IsiA18 supercomplexes allowed us to make inferences about EET from the IsiA18 ring to the PSI3 core and demonstrate that the number of entry points varies between sample preparations studied by different groups. In our most recent samples, there most likely are three entry points for EET from the IsiA18 ring per the PSI core monomer, with two of these entry points likely being located next to each other. Therefore, there are nine entry points from the IsiA18 ring to the PSI3 trimer. We anticipate that the data discussed below will stimulate further research in this area, providing even more insight into the structure-based models of these important cyanobacterial photosystems.

Feeling the Strain: Quantifying Ligand Deformation in Photosynthesis

Structural distortion of protein-bound ligands can play a critical role in enzyme function by tuning the electronic and chemical properties of the ligand molecule. However, quantifying these effects is difficult due to the limited resolution of protein structures and the difficulty of generating accurate structural restraints for nonprotein ligands. Here, we seek to quantify these effects through a statistical analysis of ligand distortion in chlorophyll proteins (CP), where ring deformation is thought to play a role in energy and electron transfer. To assess the accuracy of ring-deformation estimates from available structural data, we take advantage of the C2 symmetry of photosystem II (PSII), comparing ring-deformation estimates for equivalent sites both within and between 113 distinct X-ray and cryogenic electron microscopy PSII structures. Significantly, we find that several deformation modes exhibit considerable variability in predictions, even for equivalent monomers, down to a 2 Å resolution, to an extent that probably prevents their utilization in optical calculations. We further find that refinement restraints play a critical role in determining deformation values to resolution as low as 2 Å. However, for those modes that are well-resolved in the structural data, ring deformation in PSII is strongly conserved across all species tested from cyanobacteria to algae. These results highlight both the opportunities and limitations inherent in structure-based analyses of the bioenergetic and optical properties of CPs and other protein-ligand complexes.

Reinvestigation on primary processes of PSII-dimer from Thermosynechococcus vulcanus by femtosecond pump-probe spectroscopy

Cyanobacterial photosynthetic apparatus efficiently capture sunlight, and the energy is subsequently transferred to photosystem I (PSI) and II (PSII), to produce electrochemical potentials. PSII is a unique membrane protein complex that photo-catalyzes oxidation of water and majorly contains photosynthetic pigments of chlorophyll a and carotenoids. In the present study, the ultrafast energy transfer and charge separation dynamics of PSII from a thermophilic cyanobacterium Thermosynechococcus vulcanus were reinvestigated by femtosecond pump-probe spectroscopic measurements under low temperature and weak intensity excitation condition. The results imply the two possible models of the energy transfers and subsequent charge separation in PSII. One is the previously suggested "transfer-to-trapped limit" model. Another model suggests that the energy transfers from core CP43 and CP47 antennas to the primary electron donor ChlD1 with time-constants of 0.71 ps and 3.28 ps at 140 K (0.17 and 1.33 ps at 296 K), respectively and that the pheophytin anion (PheoD1-) is generated with the time-constant of 43.0 ps at 140 K (14.8 ps at 296 K) upon excitation into the Qy band of chlorophyll a at 670 nm. The secondary electron transfer to quinone QA: PheoD1-QA → PheoD1QA- is observed with the time-constant of 650 ps only at 296 K. On the other hand, an inefficient β-carotene → chlorophyll a energy transfer (33%) occurred after excitation to the S2 state of β-carotene at 500 nm. Instead, the carotenoid triplet state appeared in an ultrafast timescale after excitation at 500 nm.

Exciton quenching by oxidized chlorophyll Z across the two adjacent monomers in a photosystem II core dimer

This study aimed to clarify (1) which pigment in a photosystem II (PSII) core complex is responsible for the 695-nm emission at 77 K and (2) the molecular basis for the oxidation-induced fluorescence quenching in PSII. Picosecond time-resolved fluorescence dynamics was compared between the dimeric and monomeric PSII with and without addition of an oxidant. The results indicated that the excitation-energy flow to the 695-nm-emitting chlorophyll (Chl) at 36 K and 77 K was hindered upon monomerization, clearly demonstrating significant exciton migration from the Chls on one monomer to the 695-nm-emitting pigment on the adjacent monomer. Oxidation of the redox-active Chl, which is named Chl_Z caused almost equal quenching of the 684-nm and 695-nm emission bands in the dimer, and lower quenching of the 695-nm band in the monomer. These results suggested two possible scenarios responsible for the 695-nm emission band: (A) Chl11-13 pair and the oxidized Chl_ZD1 work as the 695-nm emitting Chl and the quenching site, respectively, and (B) Chl29 and the oxidized Chl_ZD2 work as the 695-nm emitting Chl and the quenching site, respectively.

Recent advances in single-molecule spectroscopy studies on light-harvesting processes in oxygenic photosynthesis

Photosynthetic light-harvesting complexes (LHCs) play a crucial role in concentrating the photon energy from the sun that otherwise excites a typical pigment molecule, such as chlorophyll-a, only several times a second. Densely packed pigments in the complexes ensure efficient energy transfer to the reaction center. At the same time, LHCs have the ability to switch to an energy-quenching state and thus play a photoprotective role under excessive light conditions. Photoprotection is especially important for oxygenic photosynthetic organisms because toxic reactive oxygen species can be generated through photochemistry under aerobic conditions. Because of the extreme complexity of the systems in which various types of pigment molecules strongly interact with each other and with the surrounding protein matrixes, there has been long-standing difficulty in understanding the molecular mechanisms underlying the flexible switching between the light-harvesting and quenching states. Single-molecule spectroscopy studies are suitable to reveal the conformational dynamics of LHCs reflected in the fluorescence properties that are obscured in ordinary ensemble measurements. Recent advanced single-molecule spectroscopy studies have revealed the dynamical fluctuations of LHCs in their fluorescence peak position, intensity, and lifetime. The observed dynamics seem relevant to the conformational plasticity required for the flexible activations of photoprotective energy quenching. In this review, we survey recent advances in the single-molecule spectroscopy study of the light-harvesting systems of oxygenic photosynthesis.

Accurate prediction of mutation-induced frequency shifts in chlorophyll proteins with a simple electrostatic model

Photosynthetic pigment-protein complexes control local chlorophyll (Chl) transition frequencies through a variety of electrostatic and steric forces. Site-directed mutations can modify this local spectroscopic tuning, providing critical insight into native photosynthetic functions and offering the tantalizing prospect of creating rationally designed Chl proteins with customized optical properties. Unfortunately, at present, no proven methods exist for reliably predicting mutation-induced frequency shifts in advance, limiting the method's utility for quantitative applications. Here, we address this challenge by constructing a series of point mutants in the water-soluble chlorophyll protein of Lepidium virginicum and using them to test the reliability of a simple computational protocol for mutation-induced site energy shifts. The protocol uses molecular dynamics to prepare mutant protein structures and the charge density coupling model of Adolphs et al. [Photosynth. Res. 95, 197-209 (2008)] for site energy prediction; a graphical interface that implements the protocol automatically is published online at http://nanohub.org/tools/pigmenthunter. With the exception of a single outlier (presumably due to unexpected structural changes), we find that the calculated frequency shifts match the experiment remarkably well, with an average error of 1.6 nm over a 9 nm spread in wavelengths. We anticipate that the accuracy of the method can be improved in the future with more advanced sampling of mutant protein structures.

The structure of photosystem I from a high-light-tolerant cyanobacteria

Photosynthetic organisms have adapted to survive a myriad of extreme environments from the earth's deserts to its poles, yet the proteins that carry out the light reactions of photosynthesis are highly conserved from the cyanobacteria to modern day crops. To investigate adaptations of the photosynthetic machinery in cyanobacteria to excessive light stress, we isolated a new strain of cyanobacteria, Cyanobacterium aponinum 0216, from the extreme light environment of the Sonoran Desert. Here we report the biochemical characterization and the 2.7 Å resolution structure of trimeric photosystem I from this high-light-tolerant cyanobacterium. The structure shows a new conformation of the PsaL C-terminus that supports trimer formation of cyanobacterial photosystem I. The spectroscopic analysis of this photosystem I revealed a decrease in far-red absorption, which is attributed to a decrease in the number of long- wavelength chlorophylls. Using these findings, we constructed two chimeric PSIs in Synechocystis sp. PCC 6803 demonstrating how unique structural features in photosynthetic complexes can change spectroscopic properties, allowing organisms to thrive under different environmental stresses.

Absence of far-red emission band in aggregated core antenna complexes

Reported herein is a Stark fluorescence spectroscopy study performed on photosystem II core antenna complexes CP43 and CP47 in their native and aggregated states. The systematic mathematical modeling of the Stark fluorescence spectra with the aid of conventional Liptay formalism revealed that induction of aggregation in both the core antenna complexes via detergent removal results in a single quenched species characterized by a remarkably broad and inhomogenously broadened emission lineshape peaking around 700 nm. The quenched species possesses a fairly large magnitude of charge-transfer character. From the analogy with the results from aggregated peripheral antenna complexes, the quenched species is thought to originate from the enhanced chlorophyll-chlorophyll interaction due to aggregation. However, in contrast, aggregation of both core antenna complexes did not produce a far-red emission band at ∼730 nm, which was identified in most of the aggregated peripheral antenna complexes. The 730-nm emission band of the aggregated peripheral antenna complexes was attributed to the enhanced chlorophyll-carotenoid (lutein1) interaction in the terminal emitter locus. Therefore, it is very likely that the no occurrence of the far-red band in the aggregated core antenna complexes is directly related to the absence of lutein1 in their structures. The absence of the far-red band also suggests the possibility that aggregation-induced conformational change of the core antenna complexes does not yield a chlorophyll-carotenoid interaction associated energy dissipation channel.

Exciton Lifetime Distributions and Population Dynamics in the FMO Protein Complex from Prosthecochloris aestuarii

Significant protein rearrangement upon excitation and energy transfer in Fenna-Matthews-Olson protein of Prosthecochloris aestuarii results in a modified energy landscape, which induces more changes in pigment site energies than predicted by the "standard" hole-burning theory. The energy changes are elucidated by simulations while investigating the effects of site-dependent disorder, both static (site-energy distribution widths) and dynamic (spectral density shapes). The resulting optimized site energies and their fluctuations are consistent with relative differences observed in inhomogeneous widths calculated by recent molecular dynamic simulations. Two sets of different spectral densities reveal how their shapes affect the population dynamics and distribution of exciton lifetimes. Calculations revealed the wavelength-dependent distributions of exciton lifetimes (T ₁) in the femtosecond to picosecond time frame. We suggest that the calculated multimodal and asymmetric wavelength-dependent T ₁ distributions offer more insight into the interpretation of resonant hole-burned (HB) spectra, kinetic traces in two-dimensional (2D) electronic spectroscopy experiments, and widely used global analyses in fitting data from transient absorption experiments.

Chlorophyll excitation energies and structural stability of the CP47 antenna of photosystem II: a case study in the first-principles simulation of light-harvesting complexes

Natural photosynthesis relies on light harvesting and excitation energy transfer by specialized pigment-protein complexes. Their structure and the electronic properties of the embedded chromophores define the mechanisms of energy transfer. An important example of a pigment-protein complex is CP47, one of the integral antennae of the oxygen-evolving photosystem II (PSII) that is responsible for efficient excitation energy transfer to the PSII reaction center. The charge-transfer excitation induced among coupled reaction center chromophores resolves into charge separation that initiates the electron transfer cascade driving oxygenic photosynthesis. Mapping the distribution of site energies among the 16 chlorophyll molecules of CP47 is essential for understanding excitation energy transfer and overall antenna function. In this work, we demonstrate a multiscale quantum mechanics/molecular mechanics (QM/MM) approach utilizing full time-dependent density functional theory with modern range-separated functionals to compute for the first time the excitation energies of all CP47 chlorophylls in a complete membrane-embedded cyanobacterial PSII dimer. The results quantify the electrostatic effect of the protein on the site energies of CP47 chlorophylls, providing a high-level quantum chemical excitation profile of CP47 within a complete computational model of "near-native" cyanobacterial PSII. The ranking of site energies and the identity of the most red-shifted chlorophylls (B3, followed by B1) differ from previous hypotheses in the literature and provide an alternative basis for evaluating past approaches and semiempirically fitted sets. Given that a lot of experimental studies on CP47 and other light-harvesting complexes utilize extracted samples, we employ molecular dynamics simulations of isolated CP47 to identify which parts of the polypeptide are most destabilized and which pigments are most perturbed when the antenna complex is extracted from PSII. We demonstrate that large parts of the isolated complex rapidly refold to non-native conformations and that certain pigments (such as chlorophyll B1 and β-carotene h1) are so destabilized that they are probably lost upon extraction of CP47 from PSII. The results suggest that the properties of isolated CP47 are not representative of the native complexed antenna. The insights obtained from CP47 are generalizable, with important implications for the information content of experimental studies on biological light-harvesting antenna systems.

Delocalization Effects in Chlorophyll Fluorescence: Nonperturbative Line Shape Analysis of a Vibronically Coupled Dimer

Non-adiabatic vibrational/electronic (vibronic) interactions in photosynthetic pigment/protein complexes (PPCs) have recently attracted considerable interest as a potential source for long-lived dynamic coherence and optimized light harvesting. The analysis of such effects is limited, however, by the complexity of the vibrational spectrum of biological pigments such as chlorophyll (Chl) molecules, which often makes numerical calculations prohibitively expensive and complicates the interpretation of experimental spectroscopic data. This work contributes to both challenges by using numerically exact computational methods to systematically examine vibronic mixing effects in the low-temperature fluorescence spectra of a Chl dimer possessing a full complement of local vibrations, using parameters extracted from experimental data. The results highlight the varying roles local vibrations can play in energy-transfer dynamics, both enhancing delocalization through vibronic resonance and, conversely, inducing dynamic localization by acting as a "self-bath" for local electronic transitions. In the specific context of line-narrowed fluorescence, the results indicate that, while low-frequency features are strongly suppressed by delocalization, high-frequency modes are likely to be dynamically localized in the parameter regime relevant to most photosynthetic complexes.

Red shift in the spectrum of a chlorophyll species is essential for the drought-induced dissipation of excess light energy in a poikilohydric moss, Bryum argenteum

Some mosses are extremely tolerant of drought stress. Their high drought tolerance relies on their ability to effectively dissipate absorbed light energy to heat under dry conditions. The energy dissipation mechanism in a drought-tolerant moss, Bryum argenteum, has been investigated using low-temperature picosecond time-resolved fluorescence spectroscopy. The results are compared between moss thalli samples harvested in Antarctica and in Japan. Both samples show almost the same quenching properties, suggesting an identical drought tolerance mechanism for the same species with two completely different habitats. A global target analysis was applied to a large set of data on the fluorescence-quenching dynamics for the 430-nm (chlorophyll-a selective) and 460-nm (chlorophyll-b and carotenoid selective) excitations in the temperature region from 5 to 77 K. This analysis strongly suggested that the quencher is formed in the major peripheral antenna of photosystem II, whose emission spectrum is significantly broadened and red-shifted in its quenched form. Two emission components at around 717 and 725 nm were assigned to photosystem I (PS I). The former component at around 717 nm is mildly quenched and probably bound to the PS I core complex, while the latter at around 725 nm is probably bound to the light-harvesting complex. The dehydration treatment caused a blue shift of the PS I emission peak via reduction of the exciton energy flow to the pigment responsible for the 725 nm band.

Role of missing carotenoid in reducing the fluorescence of single monomeric photosystem II core complexes

The fluorescence of monomeric photosystem II core complexes (mPSIIcc) of the cyanobacterium Thermosynechococcus elongatus, originating from redissolved crystals, is investigated by using single-molecule spectroscopy (SMS) at 1.6 K. The emission spectra of individual mPSIIcc are dominated by sharp zero-phonon lines, showing the existence of different emitters compatible with the F685, F689, and F695 bands reported formerly. The intensity of F695 is reduced in single mPSIIcc as compared to single PSIIcc-dimers (dPSIIcc). Crystal structures show that one of the β-carotene (β-Car) cofactors located at the monomer-monomer interface in dPSIIcc is missing in mPSIIcc. This β-Car in dPSIIcc is in van der Waals distance to chlorophyll (Chl) 17 in the CP47 subunit. We suggest that this Chl contributes to the F695 emitter. A loss of β-Car cofactors in mPSIIcc preparations will lead to an increased lifetime of the triplet state of Chl 17, which can explain the reduced singlet emission of F695 as observed in SMS.

Ultrafast energy transfer within the photosystem II core complex

We report 2D electronic spectroscopy on the photosystem II core complex (PSII CC) at 77 K under different polarization conditions. A global analysis of the high time-resolution 2D data shows rapid, sub-100 fs energy transfer within the PSII CC. It also reveals the 2D spectral signatures of slower energy equilibration processes occurring on several to hundreds of picosecond time scales that are consistent with previous work. Using a recent structure-based model of the PSII CC [Y. Shibata, S. Nishi, K. Kawakami, J. R. Shen and T. Renger, J. Am. Chem. Soc., 2013, 135, 6903], we simulate the energy transfer in the PSII CC by calculating auxiliary time-resolved fluorescence spectra. We obtain the observed sub-100 fs evolution, even though the calculated electronic energy shows almost no dynamics at early times. On the other hand, the electronic-vibrational interaction energy increases considerably over the same time period. We conclude that interactions with vibrational degrees of freedom not only induce population transfer between the excitonic states in the PSII CC, but also reshape the energy landscape of the system. We suggest that the experimentally observed ultrafast energy transfer is a signature of excitonic-polaron formation.

Fluorescence property of photosystem II protein complexes bound to a gold nanoparticle

Development of an efficient photo-anode system for water oxidation is key to the success of artificial photosynthesis. We previously assembled photosystem II (PSII) proteins, which are an efficient natural photocatalyst for water oxidation, on a gold nanoparticle (GNP) to prepare a PSII-GNP conjugate as an anode system in a light-driven water-splitting nano-device (Noji et al., J. Phys. Chem. Lett., 2011, 2, 2448-2452). In the current study, we characterized the fluorescence property of the PSII-GNP conjugate by static and time-resolved fluorescence measurements, and compared with that of free PSII proteins. It was shown that in a static fluorescence spectrum measured at 77 K, the amplitude of a major peak at 683 nm was significantly reduced and a red shoulder at 693 nm disappeared in PSII-GNP. Time-resolved fluorescence measurements showed that picosecond components at 683 nm decayed faster by factors of 1.4-2.1 in PSII-GNP than in free PSII, explaining the observed quenching of the major fluorescence peak. In addition, a nanosecond-decay component arising from a 'red chlorophyll' at 693 nm was lost in time-resolved fluorescence of PSII-GNP, probably due to a structural perturbation of this chlorophyll by interaction with GNP. Consistently with these fluorescence properties, degradation of PSII during strong-light illumination was two times slower in PSII-GNP than in free PSII. The enhanced durability of PSII is an advantageous property of the PSII-GNP conjugate in the development of an artificial photosynthesis device.

Toward an Understanding of the Excitonic Structure of the CP47 Antenna Protein Complex of Photosystem II Revealed via Circularly Polarized Luminescence

Identification of the lowest energy pigments in the photosynthetic CP47 antenna protein complex of Photosystem II (PSII) is essential for understanding its excitonic structure, as well as excitation energy pathways in the PSII core complex. Unfortunately, there is no consensus concerning the nature of the low-energy state(s), nor chlorophyll (Chl) site energies in this important photosynthetic antenna. Although we raised concerns regarding the estimations of Chl site energies obtained from modeling studies of various types of CP47 optical spectra [Reinot, T; et al., Anal. Chem. Insights 2016, 11, 35-48] recent new assignments imposed by the shape of the circularly polarized luminescence (CPL) spectrum [Hall, J.; et al., Biochim. Biophys. Acta 2016, 1857, 1580-1593] necessitate our comments. We demonstrate that other combinations of low-energy Chls provide equally good or improved simultaneous fits of various optical spectra (absorption, emission, CPL, circular dichroism, and nonresonant hole-burned spectra), but more importantly, we expose the heterogeneous nature of the recently studied complexes and argue that the published composite nature of the CPL (contributed to by CPL₆₈₅, CPL₆₉₁, and CPL₆₉₅) does not represent an intact CP47 protein. A positive CPL₆₉₅ is extracted for the intact protein, which, when simultaneously fitted with multiple other optical spectra, provides new information on the excitonic structure of intact and destabilized CP47 complexes and their lowest energy state(s).

Frequently asked questions about chlorophyll fluorescence, the sequel

Using chlorophyll (Chl) a fluorescence many aspects of the photosynthetic apparatus can be studied, both in vitro and, noninvasively, in vivo. Complementary techniques can help to interpret changes in the Chl a fluorescence kinetics. Kalaji et al. (Photosynth Res 122:121-158, 2014a) addressed several questions about instruments, methods and applications based on Chl a fluorescence. Here, additional Chl a fluorescence-related topics are discussed again in a question and answer format. Examples are the effect of connectivity on photochemical quenching, the correction of F V /F M values for PSI fluorescence, the energy partitioning concept, the interpretation of the complementary area, probing the donor side of PSII, the assignment of bands of 77 K fluorescence emission spectra to fluorescence emitters, the relationship between prompt and delayed fluorescence, potential problems when sampling tree canopies, the use of fluorescence parameters in QTL studies, the use of Chl a fluorescence in biosensor applications and the application of neural network approaches for the analysis of fluorescence measurements. The answers draw on knowledge from different Chl a fluorescence analysis domains, yielding in several cases new insights.

The lowest-energy chlorophyll of photosystem II is adjacent to the peripheral antenna: Emitting states of CP47 assigned via circularly polarized luminescence

The identification of low-energy chlorophyll pigments in photosystem II (PSII) is critical to our understanding of the kinetics and mechanism of this important enzyme. We report parallel circular dichroism (CD) and circularly polarized luminescence (CPL) measurements at liquid helium temperatures of the proximal antenna protein CP47. This assembly hosts the lowest-energy chlorophylls in PSII, responsible for the well-known "F695" fluorescence band of thylakoids and PSII core complexes. Our new spectra enable a clear identification of the lowest-energy exciton state of CP47. This state exhibits a small but measurable excitonic delocalization, as predicated by its CD and CPL. Using structure-based simulations incorporating the new spectra, we propose a revised set of site energies for the 16 chlorophylls of CP47. The significant difference from previous analyses is that the lowest-energy pigment is assigned as Chl 612 (alternately numbered Chl 11). The new assignment is readily reconciled with the large number of experimental observations in the literature, while the most common previous assignment for the lowest energy pigment, Chl 627(29), is shown to be inconsistent with CD and CPL results. Chl 612(11) is near the peripheral light-harvesting system in higher plants, in a lumen-exposed region of the thylakoid membrane. The low-energy pigment is also near a recently proposed binding site of the PsbS protein. This result consequently has significant implications for our understanding of the kinetics and regulation of energy transfer in PSII.

On the Conflicting Estimations of Pigment Site Energies in Photosynthetic Complexes: A Case Study of the CP47 Complex

We focus on problems with elucidation of site energies (E0n) for photosynthetic complexes (PSCs) in order to raise some genuine concern regarding the conflicting estimations propagating in the literature. As an example, we provide a stern assessment of the site energies extracted from fits to optical spectra of the widely studied CP47 antenna complex of photosystem II from spinach, though many general comments apply to other PSCs as well. Correct values of E0n for chlorophyll (Chl) a in CP47 are essential for understanding its excitonic structure, population dynamics, and excitation energy pathway(s). To demonstrate this, we present a case study where simultaneous fits of multiple spectra (absorption, emission, circular dichroism, and nonresonant hole-burned spectra) show that several sets of parameters can fit the spectra very well. Importantly, we show that variable emission maxima (690–695 nm) and sample-dependent bleaching in nonresonant hole-burning spectra reported in literature could be explained, assuming that many previously studied CP47 samples were a mixture of intact and destabilized proteins. It appears that the destabilized subpopulation of CP47 complexes could feature a weakened hydrogen bond between the 13¹-keto group of Chl29 and the PsbH protein subunit, though other possibilities cannot be entirely excluded, as discussed in this work. Possible implications of our findings are briefly discussed.

Structure-Based Modeling of Fluorescence Kinetics of Photosystem II: Relation between Its Dimeric Form and Photoregulation

A photosystem II-enriched membrane (PSII-em) consists of the PSII core complex (PSII-cc) which is surrounded by peripheral antenna complexes. PSII-cc consists of two core antenna (CP43 and CP47) and the reaction center (RC) complex. Time-resolved fluorescence spectra of a PSII-em were measured at 77 K. The data were globally analyzed with a new compartment model, which has a minimum number of compartments and is consistent with the structure of PSII-cc. The reliability of the model was investigated by fitting the data of different experimental conditions. From the analysis, the energy-transfer time constants from the peripheral antenna to CP47 and CP43 were estimated to be 20 and 35 ps, respectively. With an exponential time constant of 320 ps, the excitation energy was estimated to accumulate in the reddest chlorophyll (Red Chl), giving a 692 nm fluorescence peak. The excited state on the Red Chl was confirmed to be quenched upon the addition of an oxidant, as reported previously. The calculations based on the Förster theory predicted that the excitation energy on Chl29 is quenched by ChlZD1(+), which is a redox active but not involved in the electron-transfer chain, located in the D1 subunit of RC, in the other monomer with an exponential time constant of 75 ps. This quenching pathway is consistent with our structure-based simulation of PSII-cc, which assigned Chl29 as the Red Chl. On the other hand, the alternative interpretation assigning Chl26 as the Red Chl was not excluded. The excited Chl26 was predicted to be quenched by another redox active ChlZD2(+) in the D2 subunit of RC in the same monomer unit with an exponential time constant of 88 ps.

Interaction of the PsbH subunit with a chlorophyll bound to histidine 114 of CP47 is responsible for the red 77K fluorescence of Photosystem II

A characteristic feature of the active Photosystem II (PSII) complex is a red-shifted low temperature fluorescence emission at about 693nm. The origin of this emission has been attributed to a monomeric 'red' chlorophyll molecule located in the CP47 subunit. However, the identity and function of this chlorophyll remain uncertain. In our previous work, we could not detect the red PSII emission in a mutant of the cyanobacterium Synechocystis sp. PCC 6803 lacking PsbH, a small transmembrane subunit bound to CP47. However, it has not been clear whether the PsbH is structurally essential for the red emission or the observed effect of mutation has been indirectly caused by compromised PSII stability and function. In the present work we performed a detailed spectroscopic characterization of PSII in cells of a mutant lacking PsbH and Photosystem I and we also characterized PSII core complexes isolated from this mutant. In addition, we purified and characterized the CP47 assembly modules containing and lacking PsbH. The results clearly confirm an essential role of PsbH in the origin of the PSII red emission and also demonstrate that PsbH stabilizes the binding of one β-carotene molecule in PSII. Crystal structures of the cyanobacterial PSII show that PsbH directly interacts with a single monomeric chlorophyll ligated by the histidine 114 residue of CP47 and we conclude that this peripheral chlorophyll hydrogen-bonded to PsbH is responsible for the red fluorescence state of CP47. Given the proximity of β-carotene this state could participate in the dissipation of excessive light energy.

Critical assessment of the emission spectra of various photosystem II core complexes

We evaluate low-temperature (low-T) emission spectra of photosystem II core complexes (PSII-cc) previously reported in the literature, which are compared with emission spectra of PSII-cc obtained in this work from spinach and for dissolved PSII crystals from Thermosynechococcus (T.) elongatus. This new spectral dataset is used to interpret data published on membrane PSII (PSII-m) fragments from spinach and Chlamydomonas reinhardtii, as well as PSII-cc from T. vulcanus and intentionally damaged PSII-cc from spinach. This study offers new insight into the assignment of emission spectra reported on PSII-cc from different organisms. Previously reported spectra are also compared with data obtained at different saturation levels of the lowest energy state(s) of spinach and T. elongatus PSII-cc via hole burning in order to provide more insight into emission from bleached and/or photodamaged complexes. We show that typical low-T emission spectra of PSII-cc (with closed RCs), in addition to the 695 nm fluorescence band assigned to the intact CP47 complex (Reppert et al. J Phys Chem B 114:11884-11898, 2010), can be contributed to by several emission bands, depending on sample quality. Possible contributions include (i) a band near 690-691 nm that is largely reversible upon temperature annealing, proving that the band originates from CP47 with a bleached low-energy state near 693 nm (Neupane et al. J Am Chem Soc 132:4214-4229, 2010; Reppert et al. J Phys Chem B 114:11884-11898, 2010); (ii) CP43 emission at 683.3 nm (not at 685 nm, i.e., the F685 band, as reported in the literature) (Dang et al. J Phys Chem B 112:9921-9933, 2008; Reppert et al. J Phys Chem B 112:9934-9947, 2008); (iii) trap emission from destabilized CP47 complexes near 691 nm (FT1) and 685 nm (FT2) (Neupane et al. J Am Chem Soc 132:4214-4229, 2010); and (iv) emission from the RC pigments near 686-687 nm. We suggest that recently reported emission of single PSII-cc complexes from T. elongatus may not represent intact complexes, while those obtained for T. elongatus presented in this work most likely represent intact PSII-cc, since they are nearly indistinguishable from emission spectra obtained for various PSII-m fragments.

Variation of exciton-vibrational coupling in photosystem II core complexes from Thermosynechococcus elongatus as revealed by single-molecule spectroscopy

The spectral properties and dynamics of the fluorescence emission of photosystem II core complexes are investigated by single-molecule spectroscopy at 1.6 K. The emission spectra are dominated by sharp zero-phonon lines (ZPLs). The sharp ZPLs are the result of weak to intermediate exciton-vibrational coupling and slow spectral diffusion. For several data sets, it is possible to surpass the effect of spectral diffusion by applying a shifting algorithm. The increased signal-to-noise ratio enables us to determine the exciton-vibrational coupling strength (Huang-Rhys factor) with high precision. The Huang-Rhys factors vary between 0.03 and 0.8. The values of the Huang-Rhys factors show no obvious correlation between coupling strength and wavelength position. From this result, we conclude that electrostatic rather than exchange or dispersive interactions are the main contributors to the exciton-vibrational coupling in this system.

Carotenoid triplet states in photosystem II: coupling with low-energy states of the core complex

The photo-excited triplet states of carotenoids, sensitised by triplet-triplet energy transfer from the chlorophyll triplet states, have been investigated in the isolated Photosystem II (PSII) core complex and PSII-LHCII (Light Harvesting Complex II) supercomplex by Optically Detected Magnetic Resonance techniques, using both fluorescence (FDMR) and absorption (ADMR) detection. The absence of Photosystem I allows us to reach the full assignment of the carotenoid triplet states populated in PSII under steady state illumination at low temperature. Five carotenoid triplet ((3)Car) populations were identified in PSII-LHCII, and four in the PSII core complex. Thus, four (3)Car populations are attributed to β-carotene molecules bound to the core complex. All of them show associated fluorescence emission maxima which are relatively red-shifted with respect to the bulk emission of both the PSII-LHCII and the isolated core complexes. In particular the two populations characterised by Zero Field Splitting parameters |D|=0.0370-0.0373 cm(-1)/|E|=0.00373-0.00375 cm(-1) and |D|=0.0381-0.0385 cm(-1)/|E|=0.00393-0.00389 cm(-1), are coupled by singlet energy transfer with chlorophylls which have a red-shifted emission peaking at 705 nm. This observation supports previous suggestions that pointed towards the presence of long-wavelength chlorophyll spectral forms in the PSII core complex. The fifth (3)Car component is observed only in the PSII-LHCII supercomplex and is then assigned to the peripheral light harvesting system.

Modeling of fluorescence line-narrowed spectra in weakly coupled dimers in the presence of excitation energy transfer

This work describes simple analytical formulas to describe the fluorescence line-narrowed (FLN) spectra of weakly coupled chromophores in the presence of excitation energy transfer (EET). Modeling studies for dimer systems (assuming low fluence and weak coupling) show that the FLN spectra (including absorption and emission spectra) calculated for various dimers using our model are in good agreement with spectra calculated by: (i) the simple convolution method and (ii) the more rigorous treatment using the Redfield approach [T. Renger and R. A. Marcus, J. Chem. Phys. 116, 9997 (2002)]. The calculated FLN spectra in the presence of EET of all three approaches are very similar. We argue that our approach provides a simplified and computationally more efficient description of FLN spectra in the presence of EET. This method also has been applied to FLN spectra obtained for the CP47 antenna complex of Photosystem II reported by Neupane et al. [J. Am. Chem. Soc. 132, 4214 (2010)], which indicated the presence of uncorrelated EET between pigments contributing to the two lowest energy (overlapping) exciton states, each mostly localized on a single chromophore. Calculated and experimental FLN spectra for CP47 complex show very good qualitative agreement.

Selective and differential optical spectroscopies in photosynthesis

Photosynthetic pigments are inherently intense optical absorbers and have strong polarisation characteristics. They can also luminesce strongly. These properties have led optical spectroscopies to be, quite naturally, key techniques in photosynthesis. However, there are typically many pigments in a photosynthetic assembly, which when combined with the very significant inhomogeneous and homogeneous linewidths characteristic of optical transitions, leads to spectral congestion. This in turn has made it difficult to provide a definitive and detailed electronic structure for many photosynthetic assemblies. An electronic structure is, however, necessary to provide a foundation for any complete description of fundamental processes in photosynthesis, particularly those in reaction centres. A wide range of selective and differential spectral techniques have been developed to help overcome the problems of spectral complexity and congestion. The techniques can serve to either reduce spectral linewidths and/or extract chromophore specific information from unresolved spectral features. Complementary spectral datasets, generated by a number of techniques, may then be combined in a 'multi-dimensional' theoretical analysis so as to constrain and define effective models of photosynthetic assemblies and their fundamental processes. A key example is the work of Renger and his group (Raszewski, Biophys J 88(2):986-998, 2005) on PS II reaction centre assemblies. This article looks to provide an overview of some of these techniques and indicate where their strengths and weaknesses may lie. It highlights some of our own contributions and indicates areas where progress may be possible.

Photosystem II does not possess a simple excitation energy funnel: time-resolved fluorescence spectroscopy meets theory

The experimentally obtained time-resolved fluorescence spectra of photosystem II (PS II) core complexes, purified from a thermophilic cyanobacterium Thermosynechococcus vulcanus, at 5–180 K are compared with simulations. Dynamic localization effects of excitons are treated implicitly by introducing exciton domains of strongly coupled pigments. Exciton relaxations within a domain and exciton transfers between domains are treated on the basis of Redfield theory and generalized Förster theory, respectively. The excitonic couplings between the pigments are calculated by a quantum chemical/electrostatic method (Poisson-TrEsp). Starting with previously published values, a refined set of site energies of the pigments is obtained through optimization cycles of the fits of stationary optical spectra of PS II. Satisfactorily agreement between the experimental and simulated spectra is obtained for the absorption spectrum including its temperature dependence and the linear dichroism spectrum of PS II core complexes (PS II-CC). Furthermore, the refined site energies well reproduce the temperature dependence of the time-resolved fluorescence spectrum of PS II-CC, which is characterized by the emergence of a 695 nm fluorescence peak upon cooling down to 77 K and the decrease of its relative intensity upon further cooling below 77 K. The blue shift of the fluorescence band upon cooling below 77 K is explained by the existence of two red-shifted chlorophyll pools emitting at around 685 and 695 nm. The former pool is assigned to Chl45 or Chl43 in CP43 (Chl numbering according to the nomenclature of Loll et al. Nature2005, 438, 1040) while the latter is assigned to Chl29 in CP47. The 695 nm emitting chlorophyll is suggested to attract excitations from the peripheral light-harvesting complexes and might also be involved in photoprotection.

Spectral shift mechanisms of chlorophylls in liquids and proteins

Origins of non-excitonic spectral shifts of chlorophylls that can reach -1,000 cm(-1) in pigment-protein complexes are actively debated in literature. We investigate possible shift mechanisms, basing on absorption and fluorescence measurements in large number of liquids. Transition wavelength in solvent-free state was estimated (±2 nm) for chlorophyll a (Chl a, 647 nm), Chl b (624 nm), bacteriochlorophyll a (BChl a, 752 nm), and pheophytines. The dispersive-repulsive shift is a predominating mechanism. It depends on polarizability difference between the ground and the excited state Δα and the Lorenz-Lorentz function of refractive index of solvent (n). The approximate (± 2Å(3)) increase of polarizability Δα is close to 15Å(3) for S(1) bands of Chl a, BChl a, and BPheo a, slightly larger for Chl b (18Å(3)), and less for Pheo a (11Å(3)). The effect of solvent polarity, expressed in terms of static dielectric permittivity (ε) is relatively minor, but characteristic for different pigments and transitions. Remarkably, maximum influence of ε on S(1) band of BChl a is less (-20 ± 10 cm(-1)) than that for Chl a (-50 ± 10 cm(-1)), and not correlated with dipole moment changes on excitation Δμ (∼2D and 0.1 ± 0.1D, respectively). Hydrogen bonding in protic solvents produces red shifts in Chl a (-60 cm(-1)) and BChl a (-100 cm(-1)), but not in Chl b. Second axial ligand of BChl a has no influence on the S(1) band, whereas the S(2) transition suffers a -400 to -600 cm(-1) down shift. Aromatic character of solvent is responsible for a ∼-100 cm(-1) red shift of both Q transitions in BChl a. The S(1) bands in chlorophylls are relatively insensitive with respect to dielectric properties and specific solvation. Therefore, nontrivial mechanisms, yielding large site-energy shifts are expected in photosynthetic chlorophyll-proteins.

Probing Electron-Transfer Times in Photosynthetic Reaction Centers by Hole-Burning Spectroscopy

A brief discussion is presented of transient hole-burned (HB) spectra (and the information that they provide) obtained for isolated reaction centers (RCs) from wild-type (WT) Rhodobacter sphaeroides, RCs containing zinc-bacteriochlorophylls (Zn-BChls), and RCs of Photosystem II (PSII) from spinach and Chlamydomonas reinhardtii . The shape of the spectral density and the strength of electron-phonon coupling in bacterial RCs are discussed. We focus, however, on heterogeneity of isolated PS II RCs from spinach and, in particular, Chlamydomonas reinhardtii , site energies of active (electron acceptor) and inactive pheophytins, the nature of the primary electron donor(s), and the possibility of multiple charge-separation (CS) pathways in the isolated PSII RC. We conclude with comments on current efforts in HB spectroscopy in the area of photosynthesis and future directions in HB spectroscopy.

Site energies of active and inactive pheophytins in the reaction center of Photosystem II from Chlamydomonas reinhardtii

It is widely accepted that the primary electron acceptor in various Photosystem II (PSII) reaction center (RC) preparations is pheophytin a (Pheo a) within the D1 protein (Pheo(D1)), while Pheo(D2) (within the D2 protein) is photochemically inactive. The Pheo site energies, however, have remained elusive, due to inherent spectral congestion. While most researchers over the past two decades placed the Q(y)-states of Pheo(D1) and Pheo(D2) bands near 678-684 and 668-672 nm, respectively, recent modeling [Raszewski et al. Biophys. J. 2005, 88, 986 - 998; Cox et al. J. Phys. Chem. B 2009, 113, 12364 - 12374] of the electronic structure of the PSII RC reversed the assignment of the active and inactive Pheos, suggesting that the mean site energy of Pheo(D1) is near 672 nm, whereas Pheo(D2) (~677.5 nm) and Chl(D1) (~680 nm) have the lowest energies (i.e., the Pheo(D2)-dominated exciton is the lowest excited state). In contrast, chemical pigment exchange experiments on isolated RCs suggested that both pheophytins have their Q(y) absorption maxima at 676-680 nm [Germano et al. Biochemistry 2001, 40, 11472 - 11482; Germano et al. Biophys. J. 2004, 86, 1664 - 1672]. To provide more insight into the site energies of both Pheo(D1) and Pheo(D2) (including the corresponding Q(x) transitions, which are often claimed to be degenerate at 543 nm) and to attest that the above two assignments are most likely incorrect, we studied a large number of isolated RC preparations from spinach and wild-type Chlamydomonas reinhardtii (at different levels of intactness) as well as the Chlamydomonas reinhardtii mutant (D2-L209H), in which the active branch Pheo(D1) is genetically replaced with chlorophyll a (Chl a). We show that the Q(x)-/Q(y)-region site energies of Pheo(D1) and Pheo(D2) are ~545/680 nm and ~541.5/670 nm, respectively, in good agreement with our previous assignment [Jankowiak et al. J. Phys. Chem. B 2002, 106, 8803 - 8814]. The latter values should be used to model excitonic structure and excitation energy transfer dynamics of the PSII RCs.

Quantum chemical description of absorption properties and excited-state processes in photosynthetic systems

The theoretical description of the initial steps in photosynthesis has gained increasing importance over the past few years. This is caused by more and more structural data becoming available for light-harvesting complexes and reaction centers which form the basis for atomistic calculations and by the progress made in the development of first-principles methods for excited electronic states of large molecules. In this Review, we discuss the advantages and pitfalls of theoretical methods applicable to photosynthetic pigments. Besides methodological aspects of excited-state electronic-structure methods, studies on chlorophyll-type and carotenoid-like molecules are discussed. We also address the concepts of exciton coupling and excitation-energy transfer (EET) and compare the different theoretical methods for the calculation of EET coupling constants. Applications to photosynthetic light-harvesting complexes and reaction centers based on such models are also analyzed.

Optical properties, excitation energy and primary charge transfer in photosystem II: theory meets experiment

In this review we discuss structure-function relationships of the core complex of photosystem II, as uncovered from analysis of optical spectra of the complex and its subunits. Based on descriptions of optical difference spectra including site directed mutagenesis we propose a revision of the multimer model of the symmetrically arranged reaction center pigments, described by an asymmetric exciton Hamiltonian. Evidence is provided for the location of the triplet state, the identity of the primary electron donor, the localization of the cation and the secondary electron transfer pathway in the reaction center. We also discuss the stationary and time-dependent optical properties of the CP43 and CP47 subunits and the excitation energy transfer and trapping-by-charge-transfer kinetics in the core complex.